The Reptilian Microbiome

The Reptilian Microbiome

In This Article

 Did you know that non-mammals comprise less than 10% of the studies on the gut microbiome? (1). There are over 10,000 species of reptiles in the world. While there are certainly differences between the species, let’s explore a little into the reptile microbiome. 

How do reptiles develop their microbiome? 

To gain further insight into what factors contribute to their microbiome development, a study examined three types of lizards native to Argentina, two omnivorous and one herbivorous. In this extensive study, they determined the microbiome varied among all species, but the two omnivorous species had more similar bacterial communities than the herbivorous species. After analyzing food sources, soil, and other environmental components, they determined that a significant amount of the bacterial communities in the gut overlapped with microbes found on the plants they consume indicating that reptiles likely acquire some of their gut bacteria from the diet.

This overlap was not seen for insects consumed. They also determined that sex and the season did not appear to significantly alter the microbiome (1). Because reptiles are ectotherms, they are very vulnerable to their environment. Another study examined the impact of environmental temperatures on the microbiome of wild-caught Western Fence Lizards. One group was exposed to temperatures of 25 degrees Celsius for the duration of the study and the other group was exposed to 25 degrees Celsius for 7 days, then 35 degrees Celsius for 10 days. Fecal samples were collected and analyzed throughout the study. They concluded that elevated temperatures led to an “expansion of variation in microbiota composition among lizard hosts” indicating that temperature does affect the microbiome (2).

Husbandry is Key

As we can see there are several environmental influences on the reptilian microbiome. Proper husbandry is of utmost importance in maintaining a healthy reptile in captivity. Lighting, temperatures, humidity, proper diet, sanitation, and suitable supplementation all need to be taken into consideration. Lack of proper husbandry can cause multiple health concerns such as secondary infections, abnormal growth, and metabolic bone disease to name a few.   

Could probiotics be a future supplement in reptile care?

One study examined the effects of probiotic administration in Yellow Bellied Sliders and Common Musk Turtles. Administration of a multiple strain probiotic and two single strain probiotics were evaluated in Yellow Bellied Sliders. It concluded that the multiple strain probiotic (MSP) and a single strain probiotic, SSPA (bacillus subtillis PB6) decreased the number of microbial agents secreted in water and enhanced the microstructure of the duodenum. In the second portion of the study, administration of MSP and SSPA to Musk Turtles determined that both probiotics improved the duodenal microstructure, but the turtles receiving the MSP had an enhanced body weight gain and increased calcium and phosphorous in turtle shells suggesting that the multiple strain probiotic contributed to improved nutrient utilization. (3)

Current research indicates the reptilian microbiome is very dependent on the host's environment. Further studies will allow us to gain better insight into the microbiome of wild and captive species which could be integral to conservation efforts. Future studies could also lead to advances in reptilian health and supplementation.


  • Kohl, Kevin D., et al. “Gut Microbial Ecology of Lizards: Insights into Diversity in the Wild, Effects of Captivity, Variation across Gut Regions and Transmission.” Molecular Ecology, vol. 26, no. 4, 2016, pp. 1175–89. Crossref, doi:10.1111/mec.13921.
  • Moeller, Andrew H., et al. “The Lizard Gut Microbiome Changes with Temperature and Is Associated with Heat Tolerance.” Applied and Environmental Microbiology, vol. 86, no. 17, 2020. ASM, doi:10.1128/aem.01181-20.
  • Rawski, Mateusz, et al. “Dietary Probiotics Affect Gastrointestinal Microbiota, Histological Structure and Shell Mineralization in Turtles.” PLOS ONE, vol. 11, no. 2, 2016, p. e0147859. PubMed, doi:10.1371/journal.pone.0147859.
Author's Name

Dr. Dana Hogg

Dr. Dana Hogg graduated in 2015 from North Carolina State University. She grew up in Wilson, North Carolina. Growing up with several animals, Dr. Hogg was drawn to the field of veterinary medicine at a young age. She completed her undergraduate degree at NCSU in 2009 and her master's degree in 2011.